1gd7

CRYSTAL STRUCTURE OF A BIFUNCTIONAL PROTEIN (CSAA) WITH EXPORT-RELATED CHAPERONE AND TRNA-BINDING ACTIVITIES.

Method: X-RAY DIFFRACTION D_max: 85.6 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gd7
沉积日期 deposition_date	2000-09-22
结构标题 title	CRYSTAL STRUCTURE OF A BIFUNCTIONAL PROTEIN (CSAA) WITH EXPORT-RELATED CHAPERONE AND TRNA-BINDING ACTIVITIES.
关键词 keywords	;OLIGONUCLEOTIDE-BINDING FOLD, FUNCTIONAL DIMER, HYDROPHOBIC CAVITY, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, RNA BINDING PROTEIN ;; RNA BINDING PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	27.19 Å
回转半径 Rg (电子) rg_electron	26.24 Å
零角强度 I(0) i0	33940600.00
分子量 molecular_weight	47604.0 kDa
排除体积 excluded_volume	60916 Å³
包络体积 envelope_volume	74617 Å³
水化壳体积 shell_volume	24337 Å³
包络直径 envelope_diameter	88.4 Å
壳层 Rg shell_rg	32.55 Å
包络 Rg envelope_rg	25.99 Å
形状 Rg shape_rg	26.24 Å
总 Rg total_rg	26.99 Å
总原子数 total_atoms	3356
残基数 n_residues	436
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	85.6 Å
Rg (实空间) rg_real	27.21 Å
Rg 误差 (实空间) rg_real_error	0.73 Å
I(0) (实空间) i0_real	3.3940e+07
I(0) 误差 (实空间) i0_real_error	5.3330e+05
Rg (倒空间) rg_reciprocal	27.21 Å
I(0) (倒空间) i0_reciprocal	33940000.0000
解质量估计 total_estimate	0.9036
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	26.6 Å
偏度 Skewness skewness	0.252
峰度 Kurtosis kurtosis	-0.706
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4381000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.973

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (2)

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1gd7a_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.4 — Myf domain

结构域编号 domain_id	d1gd7b_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.4 — Myf domain

结构域编号 domain_id	d1gd7c_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.4 — Myf domain

结构域编号 domain_id	d1gd7d_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.4 — Myf domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1gd7A00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1gd7B00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1gd7C00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	1gd7D00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	55.715 Å
晶胞边长 b length_b	55.715 Å
晶胞边长 c length_c	167.064 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 43
空间群编号 int_tables_number	78
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2190
R_work r_work	0.2170
R_free r_free	0.2770

描述 description	CSAA PROTEIN
分子量 formula_weight	11915.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	3684

CRYSTAL STRUCTURE OF A BIFUNCTIONAL PROTEIN (CSAA) WITH EXPORT-RELATED CHAPERONE AND TRNA-BINDING ACTIVITIES.

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Thermus thermophilus
NCBI 分类编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	328

fit	/app/data/saxs_computation/gd/1gd7/1gd7.fit
pddf	/app/data/pr_computation/gd/1gd7/1gd7.pr.out
profile	/app/data/saxs_computation/gd/1gd7/1gd7.dat